[2024-01-24 13:43:27,000] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:43:27,001] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:43:27,001] [INFO] DQC Reference Directory: /var/lib/cwl/stgde6be7ae-4951-4da9-b991-f5c0b3b67762/dqc_reference
[2024-01-24 13:43:28,166] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:43:28,167] [INFO] Task started: Prodigal
[2024-01-24 13:43:28,167] [INFO] Running command: gunzip -c /var/lib/cwl/stg68101c3c-1b21-4b14-aded-fb2bc859029c/GCF_001895265.1_ASM189526v1_genomic.fna.gz | prodigal -d GCF_001895265.1_ASM189526v1_genomic.fna/cds.fna -a GCF_001895265.1_ASM189526v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:31,664] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:31,664] [INFO] Task started: HMMsearch
[2024-01-24 13:43:31,665] [INFO] Running command: hmmsearch --tblout GCF_001895265.1_ASM189526v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde6be7ae-4951-4da9-b991-f5c0b3b67762/dqc_reference/reference_markers.hmm GCF_001895265.1_ASM189526v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:31,843] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:31,845] [INFO] Found 6/6 markers.
[2024-01-24 13:43:32,066] [INFO] Query marker FASTA was written to GCF_001895265.1_ASM189526v1_genomic.fna/markers.fasta
[2024-01-24 13:43:32,067] [INFO] Task started: Blastn
[2024-01-24 13:43:32,067] [INFO] Running command: blastn -query GCF_001895265.1_ASM189526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde6be7ae-4951-4da9-b991-f5c0b3b67762/dqc_reference/reference_markers.fasta -out GCF_001895265.1_ASM189526v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:32,673] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:32,676] [INFO] Selected 18 target genomes.
[2024-01-24 13:43:32,677] [INFO] Target genome list was writen to GCF_001895265.1_ASM189526v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:32,732] [INFO] Task started: fastANI
[2024-01-24 13:43:32,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg68101c3c-1b21-4b14-aded-fb2bc859029c/GCF_001895265.1_ASM189526v1_genomic.fna.gz --refList GCF_001895265.1_ASM189526v1_genomic.fna/target_genomes.txt --output GCF_001895265.1_ASM189526v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:39,527] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:39,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde6be7ae-4951-4da9-b991-f5c0b3b67762/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:39,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde6be7ae-4951-4da9-b991-f5c0b3b67762/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:39,538] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:43:39,538] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:43:39,538] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Francisella uliginis	strain=TX07-7310	GCA_001895265.1	573570	573570	type	True	100.0	745	745	95	conclusive
Francisella halioticida	strain=DSM 23729	GCA_002211785.1	549298	549298	type	True	84.5874	532	745	95	below_threshold
Francisella hispaniensis	strain=CCUG 58020	GCA_001885235.1	622488	622488	type	True	80.0882	348	745	95	below_threshold
Francisella hispaniensis	strain=CCUG 58020	GCA_001608445.1	622488	622488	type	True	80.0096	352	745	95	below_threshold
Francisella noatunensis subsp. noatunensis	strain=2005/50/F292-6	GCA_009823375.1	360196	657445	type	True	79.932	295	745	95	below_threshold
Francisella philomiragia	strain=ATCC 25015	GCA_000156715.1	28110	28110	type	True	79.8674	363	745	95	below_threshold
Francisella philomiragia	strain=O#319L	GCA_000833455.1	28110	28110	type	True	79.7681	371	745	95	below_threshold
Francisella tularensis subsp. novicida	strain=U112	GCA_000833375.1	264	263	type	True	79.6734	350	745	95	below_threshold
Francisella tularensis subsp. novicida	strain=U112	GCA_000014645.1	264	263	type	True	79.6726	348	745	95	below_threshold
Francisella persica	strain=FSC845	GCA_001275365.1	954	954	type	True	79.4371	262	745	95	below_threshold
Francisella persica	strain=ATCC VR-331	GCA_001653955.1	954	954	type	True	79.3829	268	745	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:39,540] [INFO] DFAST Taxonomy check result was written to GCF_001895265.1_ASM189526v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:39,541] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:39,541] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:39,541] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde6be7ae-4951-4da9-b991-f5c0b3b67762/dqc_reference/checkm_data
[2024-01-24 13:43:39,542] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:39,566] [INFO] Task started: CheckM
[2024-01-24 13:43:39,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001895265.1_ASM189526v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001895265.1_ASM189526v1_genomic.fna/checkm_input GCF_001895265.1_ASM189526v1_genomic.fna/checkm_result
[2024-01-24 13:43:57,013] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:57,014] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:57,034] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:57,034] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:57,034] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001895265.1_ASM189526v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:57,035] [INFO] Task started: Blastn
[2024-01-24 13:43:57,035] [INFO] Running command: blastn -query GCF_001895265.1_ASM189526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde6be7ae-4951-4da9-b991-f5c0b3b67762/dqc_reference/reference_markers_gtdb.fasta -out GCF_001895265.1_ASM189526v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:58,004] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:58,010] [INFO] Selected 8 target genomes.
[2024-01-24 13:43:58,010] [INFO] Target genome list was writen to GCF_001895265.1_ASM189526v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:58,018] [INFO] Task started: fastANI
[2024-01-24 13:43:58,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg68101c3c-1b21-4b14-aded-fb2bc859029c/GCF_001895265.1_ASM189526v1_genomic.fna.gz --refList GCF_001895265.1_ASM189526v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001895265.1_ASM189526v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:02,149] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:02,158] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:02,158] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_001895265.1	s__Francisella uliginis	100.0	745	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012224145.1	s__Francisella sp012224145	87.1	579	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008711465.1	s__Francisella sp008711465	86.6456	576	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211785.1	s__Francisella halioticida	84.5564	532	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.38	99.38	0.93	0.93	2	-
GCF_000764555.1	s__Francisella sp000764555	80.4797	365	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001885235.1	s__Francisella hispaniensis	80.0882	348	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	98.55	97.74	0.95	0.92	4	-
GCF_000156715.1	s__Francisella philomiragia	79.8596	364	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	97.81	97.38	0.91	0.88	49	-
GCF_001653955.1	s__Francisella persica	79.3152	267	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:02,160] [INFO] GTDB search result was written to GCF_001895265.1_ASM189526v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:02,161] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:02,164] [INFO] DFAST_QC result json was written to GCF_001895265.1_ASM189526v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:02,165] [INFO] DFAST_QC completed!
[2024-01-24 13:44:02,165] [INFO] Total running time: 0h0m35s